During the Burning Legion's second invasion of Azeroth during the Third War, Illidan was released by Malfurion's mate, Tyrande Whisperwind, and he clashed against the nathrezim, Tichondrius, and slew the demon. Shortly after he absorbed the power of the Skull of Gul'dan, turning him into what he is now, which forced Malfurion and Tyrande to banish him once more. Illidan traveled to Outland, where he met Lady Vashj and Kael'thas Sunstrider, and together they formed an alliance to fight the Burning Legion. Throughout this time, they also were joined by Akama. After the Battle of Mount Hyjal and the death of Archimonde at Nordassil, Illidan clashed with Arthas Menethil, and was wounded below in Icecrown, and taken back to Outland.

Eventually, the Black Temple, where the Illidari resided, was invaded by several adventurers, and Illidan was slain by Maiev Shadowsong, Akama, and the adventurers atop Black Temple, and his body was taken by Maiev to the Vault of the Wardens, beneath Azsuna on the Broken Isles.

At the beginning of the Burning Legion's third invasion of Azeroth, Illidan's body was taken by Cordana Felsong and Gul'dan from an alternate universe. Gul'dan took the body to Black Rook Hold in Val'sharah, where he performed a ritual to separate Illidan's soul from his body. Illidan's demonic soul was then sent to the Twisting Nether. Later, the Illidari made contact with his soul from the Fel Hammer. He informed them to return to the Black Temple and speak to Akama, as he knew Illidan's plan to defeat the Legion. However, Illidan was soon discovered by demons and tells demon hunter players they are in charge of the Illidari, before losing contact.

The Illidari later discovered that Sargeras was planning to use Illidan's body as his vessel on Azeroth, with Gul'dan attempting to summon Sargeras's soul through the Nightwell at the Nighthold. They attempted to take Illidan's soul from the Twisting Nether, however found that it had been moved to Helheim. After Helya was slain, Illidan's soul was placed in Light's Heart. At the Nighthold, Khadgar transferred Illidan's soul back into his body while heroes fought Gul'dan. Once Gul'dan was defeated, Illidan was freed from his fel prism and choked Gul'dan, causing him to explode with fel fire, only his skull remainining. Illidan crushed Gul'dan's skull and turned to the heroes, telling them that they had now seen what he had, and urged them to follow him into the abyss.

Illidan later helped lead the Armies of Legionfall against the Legion at the Broken Shore, and led a group alongside Maiev to explore the Cathedral of Eternal Night. Shortly after, he delved into the Tomb of Sargeras alongside Velen, Khadgar, and the Armies of Legionfall. At the bottom of the tomb, they followed Kil'jaeden through a portal to his ship in the Twisting Nether, where they permanently destroyed the eredar lord. Illidan then used the Sargerite Keystone to create a rift between Argus and Azeroth.

Shortly after the events on the Broken Shore, Illidan traveled to Azuremyst Isle to board the new draenei vessel called the Vindicaar. He, along with Velen, Khadgar, Magni Bronzebeard, and the champions of Azeroth, traveled aboard the ship to Argus, where they united with the Army of the Light, led by Turalyon and Alleria Windrunner, and a group of broken called the Argussian Reach, led by Chieftain Hatuun. After a successful campaign against the Legion on Argus, the forces of Azeroth stormed Antorus, the Burning Throne. Following the resurrection of the titan Pantheon, the defeat of Aggramar, and retrieval of Argus's world-soul, they were transported to the Seat of the Pantheon. The world-soul of Argus was transformed into the titan Argus the Unmaker, and was defeated by the forces of Azeroth. They soon headed home on the Vindicaar, but Illidan chose to stay behind at the Seat of the Pantheon. As Sargeras prepared to destroy Azeroth, the Pantheon used their power, along with Argus's remaining power, to pull Sargeras to the Seat of the Pantheon and imprison him. As the rift between Argus and Azeroth closed, Illidan prepared to face the Dark Titan.